Genome-Wide Characterization of NBS-Encoding Genes in Watermelon and Their Potential Association with Gummy Stem Blight Resistance

Identification of Key Genes Involved in Seed Germination of Astragalus mongholicus

Seed germination is a fundamental process in plant reproduction, and it involves a series of complex physiological mechanisms. The germination rate of Astragalus mongholicus (AM) seeds is significantly lower under natural conditions. To investigate the key genes associated with AM seed germination, seeds from AM plants were collected at 0, 12, 24, and 48 h for a transcriptomic analysis, weighted gene co-expression network analysis (WGCNA), and machine learning (ML) analysis. The primary pathways involved in AM seed germination include plant-pathogen interactions and plant hormone signaling. Four key genes were identified through the WGCNA and ML: Cluster-28,554.0, FAS4, T10O24.10, and EPSIN2. These findings were validated using real-time quantitative reverse transcription PCR (qRT-PCR), and results from RNA sequencing demonstrated a high degree of concordance. This study reveals, for the first time, the key genes related to AM seed germination, providing potential gene targets for further research. The discovery of N4-acetylcysteine (ac4C) modification during seed germination not only enhances our understanding of plant ac4C but also offers valuable insights for future functional research and application exploration.

Bioactivity and Resistance Risk of Fluxapyroxad, a Novel SDHI Fungicide, in Didymella bryoniae

Gummy stem blight, caused by Didymella bryoniae, is an important disease in watermelon in China. Fluxapyroxad, a new succinate dehydrogenase inhibitor fungicide, shows strong inhibition of the mycelia growth of D. bryoniae. However, its resistance risk in D. bryoniae is unclear. In this research, the sensitivities of 60 D. bryoniae strains to fluxapyroxad were investigated. The average EC50 value and MIC values of 60 D. bryoniae strains against fluxapyroxad were 0.022 ± 0.003 μg/ml and ≤0.1 μg/ml for mycelial growth, respectively. Eight fluxapyroxad-resistant mutants with medium resistance levels were acquired from three wild-type parental strains. The mycelial growth and dry weight of mycelia of most mutants were significantly lower than those of their parental strains. However, four resistant mutants showed a similar phenotype in pathogenicity compared with their parental strains. The above results demonstrated that there was a medium resistance risk for fluxapyroxad in D. bryoniae. The cross-resistance assay showed that there was positive cross-resistance between fluxapyroxad and pydiflumetofen, thifluzamide, and boscalid, but there was no cross-resistance between fluxapyroxad and tebuconazole and mepronil. These results will contribute to evaluating the resistance risk of fluxapyroxad for managing diseases caused by D. bryoniae and further increase our understanding about the mode of action of fluxapyroxad.

Gummy stem blight: One disease, three pathogens

Gummy stem blight (GSB) is a major disease of cucurbits worldwide. It is caused by three fungal species that are morphologically identical and have overlapping geographic and host ranges. Controlling GSB is challenging due to the lack of resistant cultivars and the pathogens' significant ability to develop resistance to systemic fungicides. The causal agent of GSB is recognized as a complex of three phylogenetically distinct species belonging to domain Eukaryota, kingdom Fungi, phylum Ascomycota, subphylum Pezizomycotina, class Dothideomycetes, subclass Pleosporomycetida, order Pleosporales, family Didymellaceae, genus Stagonosporopsis, species cucurbitacearum, citrulli, and caricae. Pycnidia are tan with dark rings of cells around the ostiole measuring 120-180 μm in diameter. Conidia are 6-13 μm long, hyaline, cylindrical with round ends, and non- or monoseptate. Pseudothecia are black and globose in shape and have a diameter of 125-213 μm. Ascospores are 14-18 × 4-6 μm long, hyaline, ellipsoidal with round ends, and monoseptate with a distinct constriction at the septum. Eight ascospores are found per ascus. The upper end of the apical cell is pointed, whereas the lower end of the bottom cell is blunt. Species-specific PCR primers that can be used in a multiplex conventional PCR assay are available. The GSB species complex is pathogenic to 37 species of cucurbits from 21 different genera. S. cucurbitacearum and S. citrulli are specific to cucurbits, while S. caricae is also pathogenic to papaya and babaco-mirim (Vasconcellea monoica), a related fruit. Under favourable environmental conditions, symptoms can appear 3-12 days after spore germination. Leaf spots often start at the leaf margin or extend to the margins. Spots expand and coalesce, resulting in leaf blighting. Active lesions are typically water-soaked. Cankers are observed on crowns, main stems, and vines. Red to amber gummy exudates are often seen on the stems after cankers develop on cortical tissue.

Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection

The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.

QTL associated with resistance to Stagonosporopsis citrulli in Citrullus amarus

Gummy stem blight (GSB) is a fungal disease affecting cucurbit crops, including watermelon (Citrullus lanatus), leading to significant yield losses. The disease is caused by three Stagonosporopsis species, of which Stagonosporopsis citrulli is the most common in the southeastern United States. Currently no gummy stem blight-resistant watermelon cultivars are available to growers. In this study, QTL-seq in an interspecific population developed from Sugar Baby × PI 189225 (Citrullus amarus) identified QTL on chromosomes 2, 5, 9 and 11. A novel QTL on chromosome 5 (Qgsb5.2) associated with resistance to S. citrulli (PVE = 13.3%) was confirmed by genetic mapping. KASP marker assays were developed for selection of Qgsb5.2 to allow breeders to track the allele contributing resistance to GSB, reducing the need for laborious phenotyping. Pyramiding different GSB resistance QTL could be a useful strategy to develop GSB resistant watermelon cultivars.

QTL associated with Gummy Stem Blight (GSB) resistance in watermelon

Background

Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), produces devastating symptoms on whole plants of watermelon (Citrullus lanatus) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties.

Results

In this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F₂ population developed from C. lanatus lines, ‘PI 279461’ (resistant) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1, ClGSB10.1, and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs (ClC01G014900 and ClC01G015010), two WRKY transcription factors (ClC01G014910 and ClC01G014990), and one AvrRpt-cleavage domain protein (ClC01G015130).

Conclusion

Two high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08849-2.

QTL Mapping for Gummy Stem Blight Resistance in Watermelon (Citrullus spp.)

Watermelon (Citrulluslanatus) is an economically important fruit crop worldwide. Gummy stem blight (GSB) is one of the most damaging diseases encountered during watermelon cultivation. In the present study, we identified quantitative trait loci (QTLs) associated with GSB resistance in an F2 population derived from a cross between maternal-susceptible line '920533' (C. lanatus) and the paternal-resistant line 'PI 189225' (C. amarus). The resistance of 178 F2 plants was assessed by two different evaluation methods, including leaf lesion (LL) and stem blight (SB). To analyze the QTLs associated with GSB resistance, a linkage map was constructed covering a total genetic distance of 1070.2 cM. QTL analysis detected three QTLs associated with GSB resistance on chromosome 8 and 6. Among them, two QTLs, qLL8.1 and qSB8.1 on chromosome 8 identified as major QTLs, explaining 10.5 and 10.0% of the phenotypic variations localizing at same area and sharing the same top markers for both LL and SB traits, respectively. A minor QTL, qSB6.1, explains 9.7% of phenotypic variations detected on chromosome 6 only for the SB trait. High-throughput markers were developed and validated for the selection of resistant QTLs using watermelon accessions, and commercial cultivars. Four potential candidate genes were predicted associated with GSB resistance based on the physical location of flanking markers on chromosome 8. These findings will be helpful for the development of watermelon cultivars resistant to GSB.

QTL associated with gummy stem blight resistance in watermelon

We identified QTLs associated with gummy stem blight resistance in an interspecific F_2:3 Citrullus population and developed marker assays for selection of the loci in watermelon. Gummy stem blight (GSB), caused by three Stagonosporopsis spp., is a devastating fungal disease of watermelon (Citrullus lanatus) and other cucurbits that can lead to severe yield losses. Currently, no commercial cultivars with genetic resistance to GSB in the field have been reported. Utilizing GSB-resistant cultivars would reduce yield losses, decrease the high cost of disease control, and diminish hazards resulting from frequent fungicide application. The objective of this study was to identify quantitative trait loci (QTLs) associated with GSB resistance in an F_2:3 interspecific Citrullus mapping population (N = 178), derived from a cross between Crimson Sweet (C. lanatus) and GSB-resistant PI 482276 (C. amarus). The population was phenotyped by inoculating seedlings with Stagonosporopsis citrulli 12178A in the greenhouse in two separate experiments, each with three replications. We identified three QTLs (ClGSB3.1, ClGSB5.1 and ClGSB7.1) associated with GSB resistance, explaining between 6.4 and 21.1% of the phenotypic variation. The genes underlying ClGSB5.1 includes an NBS-LRR gene (ClCG05G019540) previously identified as a candidate gene for GSB resistance in watermelon. Locus ClGSB7.1 accounted for the highest phenotypic variation and harbors twenty-two candidate genes associated with disease resistance. Among them is ClCG07G013230, encoding an Avr9/Cf-9 rapidly elicited disease resistance protein, which contains a non-synonymous point mutation in the DUF761 domain that was significantly associated with GSB resistance. High throughput markers were developed for selection of ClGSB5.1 and ClGSB7.1. Our findings will facilitate the use of molecular markers for efficient introgression of the resistance loci and development of GSB-resistant watermelon cultivars.

Molecular and Biochemical Characterization of Pydiflumetofen-Resistant Mutants of Didymella bryoniae

Gummy stem blight (GSB), caused by Didymella bryoniae, is a devastating disease on watermelon. Pydiflumetofen belongs to succinate dehydrogenase inhibitor (SDHI) fungicide, which is effective in controlling many plant diseases. The EC₅₀ values of 69 D. bryoniae isolates to pydiflumetofen ranged from 0.0018 to 0.0071 μg/mL, and the minimal inhibitory concentration (MIC) value of all strains to pydiflumetofen was <0.05 μg/mL. Eight pydiflumetofen-resistant mutants were obtained, and the level of resistance was stable. The mycelial growth, dry weight of mycelia, hyphal morphology, and pathogenicity of most resistant mutants did not change significantly compared with their parental strains, which indicated that the resistance risk of D. bryoniae to pydiflumetofen would be medium to high. Sequencing alignment showed that five resistant mutants presented a mutation at codon 277 (H277Y) in the SdhB gene. The point mutants FgSdhB^H248Y/R exhibited decreased sensitivity to pydiflumetofen in Fusarium graminearum, which indicated that the point mutants of SdhB could reduce sensitivity to pydiflumetofen. These results further increase our understanding about the mode of action and the resistance mechanism of pydiflumetofen.

Characterization of the western white pine TIR-NBS-LRR (PmTNL2) gene by transcript profiling and promoter analysis

Proteins with nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) have been reported to play important roles in plant disease resistance, growth, and development. However, no comprehensive analysis of this protein family has been performed in conifers. Here we report that the Pinus monticola PmTNL2 gene is a member of the NBS-LRR superfamily. Quantitative reverse transcription-PCR (qRT-PCR) analysis revealed that the PmTNL2 transcript was expressed in a tissue-specific pattern with extensive regulation by various environmental stimuli in western white pine seedlings, suggesting its wide involvement in stress defense and diverse developmental processes. In silico analysis of the PmTNL2 promoter region revealed multiple cis-regulatory elements characterized with potential functions for development-, light-, and stress-regulated transcript expression. Expression patterns were largely confirmed by PmTNL2 promoter-directed reporter gene expression using stable transgenic Arabidopsis plants. Notably, the PmTNL2 promoter activity was highly expressed in shoot apical and floral meristems and was induced strongly with vascular specificity by pathogen infection. Our data has provided a fundamental insight into both expression regulation and putative functions of the PmTNL2 gene in the context of plant growth and development, as well as in responses to environmental stressors. Promoter application as a potential tool for tree improvement was further discussed.